Recombinant DNA Clones Research Articles

Nm23-H1 Expression and disease recurrence after surgical resection of small hepatocellular carcinoma

Background/Aims: The nm23-H1 gene is thought to act as a metastasis-suppressor gene. This study investigates the relationship between nm23-H1 messenger RNA (mRNA) expression and intrahepatic tumor recurrence after surgical resection of small hepatocellular carcinoma. Methods: Seventeen cirrhotic patients with solitary hepatocellular carcinoma <5 cm underwent surgical resection. In 7 patients, the neoplasm recurred after a 12-month median follow-up, whereas the other 10 patients were free of disease after a 30-month median follow-up. Both groups were similar according to age, sex, etiology, status of the underlying liver, tumor size, and other pathological characteristics of the neoplasm. nm23-H1 mRNA levels were assessed in matched tumor and surrounding cirrhotic liver samples by Northern blot hybridization using a 900-base pair probe, which is a BamHI fragment of pnm23-H1 recombinant complementary DNA clone encoding the nm23-H1 human gene. Results: Eight of the 10 patients without disease recurrence during follow-up showed nm23-H1 overexpression with an increase ranging between three- and 45-fold when compared with the nontumoral surrounding liver. Only 1 of the 7 patients with tumor recurrence showed higher nm23-H1 mRNA levels in the tumor than in the nonneoplastic sample (P = 0.013). Conclusions: nm23 mRNA overexpression in small solitary hepatocellular carcinoma is associated with a lower recurrence rate after surgical resection, suggesting that this gene may participate in the metastatic dissemination of this neoplasm.

DNA cloning and screening of a partial genomic library from an arbuscular mycorrhizal fungus, Scutellospora castanea

A technique has been developed to efficiently extract purified, restrictable genomic DNA from spores of different arbuscular mycorrhizal fungi in order to begin detailed investigations of the genome of the Glomales. The protocol yielded variable amounts of DNA depending on the fungal species; for Scutellospora castanea and Gigaspora rosea it reached values of 1.5–2 ng/spore. EcoRI digests of DNA from S. castanea were cloned into pUC18 and about 1000 recombinant DNA clones were obtained. Of those screened, 50 contained inserts of 500–7000 bp. Selected inserts detected DNA sequences from S. castanea spores or roots infected by this fungus, but not from nonmycorrhizal roots. This is the first report of a partial genomic library from an arbuscular mycorrhizal fungus.

Detection and Cloning of Human Papillomavirus DNA Associated with Recurrent Respiratory Papillomatosis in Thailand

Recurrent respiratory papillomatosis (RRP) is highly prevalent in Thailand. In this study, we examined the presence of human papillomavirus (HPV) DNA in 25 RRP patients in Thailand by means of dot blot analysis and/or polymerase chain reaction. Eighty‐four percent (21/25) of cases and 4% (1/25) of cases were positive for HPV‐11 DNA and HPV‐6 DNA, respectively. Three cases (3/25) were negative for all of the examined HPV types. No cases were positive for HPV‐16 or 18. Furthermore, we isolated the recombinant HPV‐11 DNA clone from a genomic library constructed with the DNA of RRP tissue. The restriction map of the cloned HPV DNA was identical with the map of known HPV‐11 DNA. These results suggest at least that no specific HPV type or subtype is likely to be associated with RRP in Thailand.

Acetoin catabolic system of Klebsiella pneumoniae CG43: sequence, expression, and organization of the aco operon

A cosmid clone which was capable of depleting acetoin in vivo was isolated from a library of Klebsiella pneumoniae CG43 cosmids. The smallest functional subclone contained a 3.9-kb DNA fragment of the cosmid clone. Sequencing of the DNA fragment revealed three open reading frames (ORFs A, B, and C) encoding polypeptides of 34, 36, and 52 kDa, respectively. The presence of these proteins was demonstrated by expression of the recombinant DNA clone in Escherichia coli. Considerable similarities between the deduced amino acid sequences of the ORFs and those of the following enzymes were found: acetoin dissimilation enzymes, pyruvate dehydrogenase complex, 2-oxoglutarate dehydrogenase complex, and branched-chain 2-oxo acid dehydrogenase complex of various origins. Activities of these enzymes, including acetoin-dependent dichlorophenolin-dohenol oxidoreductase and dihydrolipoamide acetyltransferase, were detected in the extracts of E. coli harboring the genes encoding products of the three ORFs. Although not required for acetoin depletion in vivo, a possible fourth ORF (ORF D), located 39 nucleotides downstream of ORF C, was also identified. The deduced N-terminal sequence of the ORF D product was highly homologous to the dihydrolipoamide dehydrogenases of several organisms. Primer extension analysis identified the transcriptional start of the operon as an A residue 72 nucleotides upstream of ORF A.

Molecular Marker Diversity and Yield of Isogenic 2x and 4x Single‐Crosses of Alfalfa

The positive correlation between level of heterozygosity and yield in autotetraploid alfalfa (Medicago sativa L.) suggests that genetic diversity between parents may be related to yield of their hybrid progeny. This was tested by comparing the levels of polymorphism among parental genotypes for restriction fragments homologous to 61 recombinant DNAc lones with the yield of their single‐cross progenies. Diploid (2x) genotypes were chromosomed oubled to produce autotetraploids (4x), and these isogenic 2x and 4x genotypes were used parents to generate progenies in 4 × 4 diallels. Seeds from reciprocal crosses were bulked to produce six single‐cross families for field evaluation at each ploidy levd. Yield data of single‐crosses were collected in spaced‐plant and microplot field trials over two and three years, respectively. Genetic dissimilarities (GDs) were estimated for all pairs of the four parents by the complement the Dice coefficient calculated from 244 restriction fragments. At the diploid level, no significant associations between GD and yield of single‐cross progenies were detected; however, high correlations were detected for tetraploid progenies in microplots and spaced‐plant field trials (r = 0.69, p &lt; 0.16 and r = 0.82, p &lt; 0.05, respectively). Inconsistencies in correlations detected between GD and yields of isogenic 2x and 4x families may be related to the level of heterozygosity expected among progenies derived from heterozygous parents at different ploidy levels. Autotetrapioids have more heterozygous loci due to tetrasomic segregation than equivalent diploids, and can benefit from greater complementargye ne interactions. Although RFLP‐based GD measurements do not appear to accurately predict yield of diploid single‐cross progenies, results from this preliminary investigation suggest that molecular marker evaluation may be useful for predicting yield of tetraploid alfalfa hybrids.

A mathematically designed STS primer without any mismatches for direct sequencing of cosmid DNA clones.

We report here a new method for the direct sequencing of large DNA inserts of cosmid clones from human chromosomes using STS primers of 14 nucleotides without any mismatches, which are designed from results of a mathematical analysis. It is clear that STS primer of 14 nucleotides is optimum for direct sequencing of cosmid recombinant DNA clones. We also provide examples of direct sequencing of cosmid clones of human chromosome 21 using these STS primers.

Restriction polymorphisms and fingerprint patterns from an interspersed repetitive element of Plasmodium falciparum DNA

A recombinant DNA clone, pC4.H32, identifies distinguishable restriction fragment patterns from different Plasmodium falciparum clones. Analysis of these DNA fingerprint patterns from parasites cultivated over several years and from progeny of a P. falciparum cross showed the fingerprints to be mitotically and meiotically stable. Restriction fragments from the parents of the cross possessed sufficient polymorphism and number to generate 14 unique fingerprint patterns in 16 independent recombinant progeny. The pC4.H32 insert contains a 0.5-kb imperfectly repeated sequence found in subtelomeric regions of multiple chromosomes. Restriction site variations both within and outside of the 0.5-kb repeat contribute to the fingerprint polymorphisms. Fingerprint analysis can serve to type P. falciparum clones and can detect mislabeling and cross-contamination of parasite stocks.

Characterization of B-cell epitopes on IpaB, an invasion-associated antigen of Shigella flexneri: identification of an immunodominant domain recognized during natural infection

The invasion plasmid antigen B (IpaB), a 62-kDa plasmid-encoded protein associated with the ability of shigellae to invade epithelial cells, is the bacterial antigen most strongly and consistently recognized by the host during infection. The strong systemic and mucosal immune responses observed against this invasin prompted us to map its B-cell epitopes. For this purpose, IpaB was first overexpressed in Shigella flexneri and used to raise rabbit polyclonal antiserum and murine monoclonal antibodies, which were subsequently used to screen a lambda gt11 ipaB library. Inserts of recombinant DNA clones that were specifically recognized by the antisera and antibodies were sequenced, and three distinct determinants were identified. Further characterization of these determinants showed that they were recognized by sera from patients convalescent from shigellosis, suggesting that they are relevant to the humoral response during natural infection. Moreover, the IpaB region comprising the three determinants was systematically recognized by all sera from infected patients that we tested, whereas other regions of the protein were not. These data suggest that this region, located between amino acid residues 147 and 258, is the major immunogenic domain of the invasin in the course of natural infection.

ESTABLISHMENT OF A STABLE GLUTAMATE DECARBOXYLELASE (GAD) EXPRESSING CELL-LINE BY TRANSFECTION.

We have constructed a recombinant DNA clone containing the gene encoding glutamic acid decarboxylase (GAD), which catalyzes the synthesis of γ-aminobutyric acid (GABA). This recombinant DNA was then transfected into mouse NIH-3T3 fibroblast cells for transplantation into Swiss-Web mice. In order to construct a plasmid capable of transcribing the DNA insert in the eucaryotic cells, the GAD gene was removed from pSP65-13, and was ligated into the vector pSV2neo, which contains the SV40 early promoter, and the neomycin resistance gene. The pSV2GAD was then transfected into NIH-3T3 fibroblasts by calcium phosphate precipitation, or by electroporation. The transfected fibroblasts were then selected with antibiotic G418 for amplification. The transient expression of GAD in the transfected fibroblasts was detected by immunocytochemical staining using anti-GAD antibody. A small population of GAD immunoreactive cells were clearly stained, and were easily distinguished from the majority of unstained background cells. These GAD-immunoreactive cells were not seen in either mock-transfected, or pSV2neo-transfected cells (vector-alone control). The transfected fibroblasts were continuously selected with antibiotic G418. Six out of 35 subcultures that had GAD-positive immunostaining in the cell lines were selected. Granular GAD-positive staining was observed in the cytoplasm and fiber extensions of the transfected cell lines in varying densities. The GAD-mRNA was also detected in the subcultures by in situ hybridization using a 35S-labeled 369-nucleotide riboprobe in pBluescript. The GAD-transfected NIH-3T3 cells were then transplanted into Swiss-Web mice. Fifteen to 30 days later, transplanted animals were perfused for identification. These cells were first identified with anti-fibronectin antibody, and the adjacent sections with anti-GAD or anti-GABA antibodies. All the transplants are fibronectin-positive. Both GAD- and GABA positive cells were observed in the transplant.

Tomato necrosis and the 369 nucleotide Y satellite of cucumber mosaic virus: factors affecting satellite biological expression

To determine which factors can affect biological expression of the Y satellite RNA of cucumber mosaic virus (CMV) in tomato, three laboratories collaboratively exchanged their natural satellite variants, the corresponding recombinant DNA clones and helper virus strains, as well as tomato varieties, on which different observations previously reported were based. The effects of these materials and the influence of temperature on symptom expression were systematically studied. The results show that in a standardized tomato bioassay at 24 degrees C, the Y satellite, when supported by either CMV-1 or CMV-Y, did not induce tomato necrosis in the Rutgers variety but elicited a slower necrotic response in the Best of All variety that was variably lethal, as compared to the faster inevitably lethal response induced by a prototype necrogenic D satellite variant in both tomato varieties. At higher temperatures (26.5 to 32 degrees C) an extremely fast-killing necrosis caused by CMV-Y itself was observed. The study demonstrates that in experiments on virus symptom modulation induced by CMV satellites, the nature of the helper virus, host plant varieties, as well as the environmental conditions should be precisely defined, and the effects of each parameter change determined separately.

The chicken alpha 1 (XI) collagen gene is widely expressed in embryonic tissues.

Complementary DNA and genomic DNA clones corresponding to the chicken alpha 1 (XI) collagen gene were isolated and characterized. These recombinant DNA clones covered 2667 base pairs of the mRNA and encode 624 amino acids of the triple helical region plus the entire carboxyl-terminal propeptide. Northern blot analysis showed a major band of approximately 6.5 kilobases and a minor band of approximately 7.5 kilobases. A combination of Northern blot and in situ hybridization analyses showed that, in addition to its presence in cartilage, this mRNA also is present in a wide variety of chicken noncartilaginous embryonic tissues including brain, heart, skeletal muscle, calvaria, and skin, but was not detected in liver. Type II collagen mRNA has also been detected at low levels in these same tissues. Also, similar to the mRNA for the alpha 1 chain for type II collagen, the alpha 1 (XI) collagen mRNA is detected in limb mesenchyme prior to condensation and differentiation of the core mesenchyme into cartilage.

The human Y chromosome: overlapping DNA clones spanning the euchromatic region.

The human Y chromosome was physically mapped by assembling 196 recombinant DNA clones, each containing a segment of the chromosome, into a single overlapping array. This array included more than 98 percent of the euchromatic portion of the Y chromosome. First, a library of yeast artificial chromosome (YAC) clones was prepared from the genomic DNA of a human XYYYY male. The library was screened to identify clones containing 160 sequence-tagged sites and the map was then constructed from this information. In all, 207 Y-chromosomal DNA loci were assigned to 127 ordered intervals on the basis of their presence or absence in the YAC's, yielding ordered landmarks at an average spacing of 220 kilobases across the euchromatic region. The map reveals that Y-chromosomal genes are scattered among a patchwork of X-homologous, Y-specific repetitive, and single-copy DNA sequences. This map of overlapping clones and ordered, densely spaced markers should accelerate studies of the chromosome.

Molecular cloning and characterization of Mycobacterium paratuberculosis promoters in Escherichia coli

DNA fragments from Mycobacterium paratuberculosis were cloned in the promoter probe plasmid pKO1. Of 957 recombinant DNA clones, 24 induced synthesis of galactokinase (the reporter gene) when these plasmids were transformed into an Escherichia coli strain deficient for the enzyme. A DNA insert from one putative promoter-containing plasmid, designated pAG5, was sequenced and shown to contain, a characteristic RNA polymerase binding site, a probable ribosomal binding site and a putative open reading frame.

Characterization of species-specific repeated DNA sequences from B. nigra

The construction and characterization of two genome-specific recombinant DNA clones from B. nigra are described. Southern analysis showed that the two clones belong to a dispersed repeat family. They differ from each other in their length, distribution and sequence, though the average GC content is nearly the same (45%). These B genome-specific repeats have been used to analyse the phylogenetic relationships between cultivated and wild species of the family Brassicaceae.

Identification and characterization of B-cell epitopes of IpaC, an invasion-associated protein of Shigella flexneri.

Invasion plasmid antigen C (IpaC) is a 43-kDa plasmid-encoded protein associated with the ability of shigellae to invade epithelial cells. This protein is consistently strongly recognized by sera from convalescent patients and monkeys experimentally infected with shigellae. The strong immunogenicity of IpaC in the course of natural infection makes it a good candidate as a potentially protective antigen. To map the B-cell epitopes of this protein, the gene encoding IpaC was cloned and expressed at a high level in Escherichia coli. The partially purified recombinant protein was used to raise rabbit polyclonal antisera and murine monoclonal antibodies. A lambda gt11 ipaC gene library was screened with the antisera and antibodies. Recombinant DNA clones producing specific antigenic determinants were isolated, and the sequence of their DNA inserts was determined. The amino acid sequence of each determinant was deduced from the minimal overlap of DNA inserts of multiple antibody-positive DNA clones. Two distinct epitopes, located between amino acid residues 25 and 33 and 90 and 97, were identified. Two additional B-cell epitopes which were located between residues 297 and 349, near the carboxy-terminal end of the protein, were characterized. Each of these epitopes was also recognized by sera from convalescent humans and monkeys. Therefore, it seems likely that these epitopes are relevant to the humoral response against IpaC during natural infection.

The 14,000-molecular-weight antigen of Mycobacterium tuberculosis is related to the alpha-crystallin family of low-molecular-weight heat shock proteins.

Eight monoclonal antibodies (MAbs) directed against the 14,000-molecular-weight (14K) antigen of Mycobacterium tuberculosis reacted specifically with mycobacteria of the M. tuberculosis complex. The nucleotide sequence of the gene encoding the 14K antigen was determined by using recombinant DNA clones isolated from lambda gt11 and cosmid libraries of the M. tuberculosis genome. The DNA sequence of the 14K protein gene coded for a polypeptide of 144 amino acids with a calculated molecular mass of 16,277 Da. The 14K antigen has a marked homology with proteins belonging to the alpha-crystallin family of low-molecular-weight heat shock proteins, which includes the 18K antigen of M. leprae. The eight MAbs recognized at least four distinct epitopes localized within the following three regions of the 14K protein: amino acids 10 to 92 (MAbs F67-8 and F67-16), amino acids 41 to 92 (F159-1 and F159-11), and amino acids 41 to 144 (F23-41, F24-2, F23-49, and TB68).

Immunodetection of antibodies in sera from symptomatic and asymptomatic Chilean Chagas' disease patients with Trypanosoma cruzi recombinant antigens.

A panel of eight Trypanosoma cruzi antigens produced by recombinant DNA techniques was used to compare the reactivity of IgG specificities in the sera from 45 chronic Chagas' disease patients with different clinical symptoms (cardiac disease, gastrointestinal lesions, and combined syndrome) with those present in the sera from 55 asymptomatic patients in Chile. All of the serum samples were first characterized for antibody to T. cruzi epimastigotes by immunofluorescence assay. All of the Chagas' disease sera were reactive, but none of five healthy controls whose sera were also tested had antibodies against the fixed parasites. A dot-blot assay was then performed to evaluate the serum reactivity against recombinant DNA clones 1, 2, 13, 26, 30, 36, 54, and SAPA (shed acute phase antigen). These recombinant antigens were recognized by a large proportion of the sera collected from the Chilean patients. Ninety-five percent of the serum samples reacted with one or more of the recombinant clones. Analysis of the reactivity with individual fusion proteins showed that 88% of these sera reacted with clones 1 and 2, and 78% reacted with clone 13. Differences in reactivity to clones number 13, 30, and SAPA were observed when symptomatic and asymptomatic patients were compared. These differences in reactivity were statistically significant (P less than 0.01) according to Fisher's exact test.

Hypercard-based data management tools for molecular biologists.

I have designed a Macintosh data management system for molecular biologists. This system, called DataMinder, can be used to store information about oligonucleotides, nucleic acid or protein sequences, recombinant DNA clones, cells, reagents and protocols. DataMinder is not limited to data storage. A number of utilities for data analysis are provided, including those for the evaluation of oligonucleotides for use as hybridization probes or primers for DNA synthesis, and a variety of sequence editing features. Context-sensitive help is available on-line. DataMinder is simple to use and to customize and allows for sharing of database information across a computer network.

Genetic Interrelatedness among Clover Proliferation Mycoplasmalike Organisms (MLOs) and Other MLOs Investigated by Nucleic Acid Hybridization and Restriction Fragment Length Polymorphism Analyses

DNA was isolated from clover proliferation (CP) mycoplasmalike organism (MLO)-diseased periwinkle plants (Catharanthus roseus (L.) G. Don.) and cloned into pSP6 plasmid vectors. CP MLO-specific recombinant DNA clones were biotin labeled and used as probes in dot hybridization and restriction fragment length polymorphism analyses to study the genetic interrelatedness among CP MLO and other MLOs, including potato witches'-broom (PWB) MLO. Results from dot hybridization analyses indicated that both a Maryland strain of aster yellows and a California strain of aster yellows are distantly related to CP MLO. Elm yellows, paulownia witches'-broom, peanut witches'-broom, loofah witches'-broom, and sweet potato witches'-broom may be very distantly related, if at all, to CP MLO. A new Jersey strain of aster yellows MLO, tomato big bud MLO, clover phyllody MLO, beet leafhopper-transmitted virescence MLO, and ash yellows MLO are related to CP MLO, but PWB MLO is the most closely related. Similarity coefficients derived from restriction fragment length polymorphism analyses revealed that PWB and CP MLOs are closely related strains and thus provided direct evidence of their relatedness in contrast to reliance solely on biological characterization.

Molecular analysis of overlapping chromosomal deletions in patients with Langer-Giedion syndrome

We have obtained lymphoblastoid cell lines from three patients with Langer-Giedion syndrome who have over-lapping deletions in 8q24.1. To isolate the deletion chromosomes from their normal homologs, patient cell lines were fused with hamster cells and hybrid cells were selected for retention of human chromosome 8. These hybrid cell lines were screened for the presence of chromosome 8 by fluorescence in situ hybridization and by Southern blot hybridization. We have hybridized 31 recombinant DNA clones derived from the 8q22-qter region to Southern blots of the hybrid cell lines; 8 were found to lie within the deletion of at least one patient. One clone identified sequences that were missing from one copy of chromosome 8 in all three patients. These clones help to further define the deletions in these patients and will serve as starting points for detailed characterization of the region.